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- PDB-9va3: Solution NMR structures of hTERT DNA G-quadruplexes (G4s) in comp... -

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Basic information

Entry
Database: PDB / ID: 9va3
TitleSolution NMR structures of hTERT DNA G-quadruplexes (G4s) in complex with small molecule ZBH-01
ComponentsDNA (5'-D(*AP*AP*TP*GP*GP*GP*AP*GP*GP*GP*TP*CP*TP*GP*GP*GP*AP*GP*GP*GP*CP*C)-3')
KeywordsDNA / G-quadruplexes / Topoisomerase I / ZBH-01
Function / homology: / : / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsZeng, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Dual Targeting of Topoisomerase I and DNA G-quadruplexes Enhances Senescence Response and Chemosensitivity in Colorectal Cancer Cells
Authors: Li, Y. / Ji, D. / Jia, Y. / Liang, Y. / Wei, E. / Gao, C. / Li, Y. / Zeng, C. / Wang, L. / Wang, C. / Guo, Z. / Zhang, Y. / Zhou, M.-M. / Wu, D. / Zeng, L.
History
DepositionJun 2, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*AP*AP*TP*GP*GP*GP*AP*GP*GP*GP*TP*CP*TP*GP*GP*GP*AP*GP*GP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5924
Polymers6,9381
Non-polymers6543
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*AP*AP*TP*GP*GP*GP*AP*GP*GP*GP*TP*CP*TP*GP*GP*GP*AP*GP*GP*GP*CP*C)-3')


Mass: 6938.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-A1EQ9 / (S)-4,11-diethyl-4-hydroxy-3,14-dioxo-3,4,12,14-tetrahydro-1H-pyrano[3',4':6,7]indolizino[1,2-b]quinolin-9-yl (2-(4-methylpiperazin-1-yl)-2-oxoethyl)carbamate


Mass: 575.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H33N5O7 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-1H NOESY
222isotropic12D 1H-1H NOESY
131isotropic22D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution120 mM potassium phosphate, 70 mM potassium chloride, 90% H2O/10% D2Osample-h2o#190% H2O/10% D2O
solution220 mM potassium phosphate, 70 mM potassium chloride, 100% D2Osample-d2o#2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMpotassium phosphatenatural abundance1
70 mMpotassium chloridenatural abundance1
20 mMpotassium phosphatenatural abundance2
70 mMpotassium chloridenatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1null Not definedcondition_298_#16.51 atm298 K
2null Not definedcondition_288_#26.51 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO8001
Bruker AVANCE NEOBrukerAVANCE NEO6002

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Refinement
MethodSoftware ordinal
torsion angle dynamics1
torsion angle dynamics2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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